Package picard.util
package picard.util
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ClassDescriptionClass for parsing text files where each line consists of fields separated by whitespace.Combines multiple Picard QualityYieldMetrics files into a single file.Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.Utilities class containing methods for restricting
VariantContextandGenotypesContextobjects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.DescribesDesigns baits for hybrid selection!Set of possible design strategies for bait design.A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.TextFileParser which reads a single text file.Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.Utilities to clip the adapter sequence from a SAMRecord readUtility class to use with DbSnp files to determine is a locus is a dbSnp site.Little tuple class to contain one bitset for SNPs and another for Indels.Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.SummaryCreated by farjoun on 11/2/16.GraphUtils.Graph<Node extends Comparable<Node>>Misc utilities for working with Illumina specific files and dataDescribes adapters used on each pair of strandsTrivially simple command line program to convert an IntervalList file to a BED file.Performs variousIntervalListmanipulations.This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.General math utilitiesA collection of common math operations that work with log values.Utility for loading properties files from resources.A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairsClass which contains utility functions that use reflection.Util class for executing R scripts.A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.Class with helper methods for generating and writing SequenceDictionary objects.A class for finding the distance between a single barcode and a barcode-read (with base qualities)Parser for tab-delimited filesParse a tabbed text file in which columns are found by looking at a header line rather than by position.This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executingA utility class for dealing with unsigned types.Enum to hold the possible types of dbSnps.